Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genus Escherichia revealed by a genome-wide association study.

Marco Galardini,Erick Denamur,Sören Schubert,Alexandra Baron,Olivier Clermont,Bede Busby,Sara Dion,Pedro Beltrao,Xavier Didelot

doi:10.1371/journal.pgen.1009065

Abstract

The genus Escherichia is composed of several species and cryptic clades, including E. coli, which behaves as a vertebrate gut commensal, but also as an opportunistic pathogen involved in both diarrheic and extra-intestinal diseases. To characterize the genetic determinants of extra-intestinal virulence within the genus, we carried out an unbiased genome-wide association study (GWAS) on 370 commensal, pathogenic and environmental strains representative of the Escherichia genus phylogenetic diversity and including E. albertii (n = 7), E. fergusonii (n = 5), Escherichia clades (n = 32) and E. coli (n = 326), tested in a mouse model of sepsis. We found that the presence of the high-pathogenicity island (HPI), a ~35 kbp gene island encoding the yersiniabactin siderophore, is highly associated with death in mice, surpassing other associated genetic factors also related to iron uptake, such as the aerobactin and the sitABCD operons. We confirmed the association in vivo by deleting key genes of the HPI in E. coli strains in two phylogenetic backgrounds. We then searched for correlations between virulence, iron capture systems and in vitro growth in a subset of E. coli strains (N = 186) previously phenotyped across growth conditions, including antibiotics and other chemical and physical stressors. We found that virulence and iron capture systems are positively correlated with growth in the presence of numerous antibiotics, probably due to co-selection of virulence and resistance. We also found negative correlations between virulence, iron uptake systems and growth in the presence of specific antibiotics (i.e. cefsulodin and tobramycin), which hints at potential "collateral sensitivities" associated with intrinsic virulence. This study points to the major role of iron capture systems in the extra-intestinal virulence of the genus Escherichia.

Highlights

We found that the presence of the high-pathogenicity island (HPI), a ~35 kbp gene island encoding the yersiniabactin siderophore, is highly associated with death in mice, surpassing other associated genetic factors related to iron uptake, such as the aerobactin and the sitABCD operons
Bacterial isolates belonging to the genus Escherichia can be human commensals and opportunistic pathogens, with the ability to cause extra-intestinal infection
We have used a statistical approach called Genome-Wide Association Study (GWAS) to show how the presence of genes that encode for iron scavenging are significantly associated with the propensity of a bacterial isolate to cause extra-intestinal infections

Summary

Introduction

Members of the Escherichia genus are both commensals of vertebrates [1] and opportunistic pathogens [2] involved in a wide range of intestinal and extra-intestinal infections. Apart from the E. coli species, the genus is composed of the cryptic Escherichia clades, and the E. fergusonii and E. albertii species The latter taxa are rarely isolated in humans but are more frequently found in the environment and avian species where they can cause intestinal infections [3,4,5]. The factors associated with high mortality are mainly linked to host conditions such as age, the presence of underlying diseases and to the portal of entry, with the urinary origin being more protective. These factors outweigh those directly attributable to the bacterial agent [7,8,9,13]

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Discussion

Conclusion